National higher education systems have undergone a series of transformations in recent decades. Since the 1980s, regulatory systems governing higher education have witnessed a number of changes. In particular, there has been a shift away from a model of state control, to one of state oversight, in which the state designs a framework of rules and policy objectives for the system as a whole, and institutions have greater freedom to establish their own mission and pursue their own priorities (Neave and Van Vught 1991, quoted in Musselin and Teixeira 2014:4). The differences between one country and another in terms of the type of regulation that is adopted are the result of political and ideological factors. This study contributes to the debate by describing the transformation of two higher education systems in Latin America. Through an analysis of a series of documents, legislation, and norms, as well as media reports on the matter, the authors show how in each of the two countries, different relationships between the market, the state, and the universities have emerged, and can be explained by political factors and ideological contexts of each country. In the case of Ecuador, the definition of policies, university autonomy, and the creation of regulatory agencies allows the state’s presence and political influence to be felt, while in Peru, a market-based philosophy guides educational policy and content. Thus, in Ecuador, in contrast to Peru, the university itself is less autonomous, and the university system is governed by the principle of responsible autonomy, with limitations in the form of supervisory and quality control responsibilities distributed among public organizations, where representatives of the executive branch make up the majority of board directorships. The regulatory process is less gradual in nature, which may have hastened the closure of universities. In this sense, researchers will discuss how the different ideological contexts and relationships between social and political actors lead, on the one hand, to government-based regulation (Ecuador), and on the other, to a market-oriented framework (Peru). Although technocracy is a characteristic of both processes, there are nuances in the way the relationship between the state, market, and universities develops.